The isolation of individual boron nitride nanotubes (BNNTs) in aqueous phases has been achieved for the first time from raw materials based on the combination of peptide wrapping with a sonication procedure. Atomic force microscopic observations revealed the representative height and length of individual BNNTs. Fluorescence and infrared absorption spectra suggested the strong pi-pi interactions between BNNTs and the peptide. The absorption maxima of BNNTs were significantly blue-shifted from 200 nm for the original BNNTs to 193 nm. The modulation of the BNNT band gap with peptide wrapping promises potential applications of the peptide/BNNT complexes to various nanotechnologies.